scholarly journals PCR-generated artefact from 16S rRNA gene-specific primers

2005 ◽  
Vol 248 (2) ◽  
pp. 183-187 ◽  
Author(s):  
Catherine A. Osborne ◽  
Maja Galic ◽  
Parveen Sangwan ◽  
Peter H. Janssen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Specific Primers

scholarly journals The Termite Group I Phylum Is Highly Diverse and Widespread in the Environment

2007 ◽  
Vol 73 (20) ◽  
pp. 6682-6685 ◽  
Author(s):  
Daniel P. R. Herlemann ◽  
Oliver Geissinger ◽  
Andreas Brune
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Specific Primers ◽  
Environmental Distribution ◽  
Data Set ◽  
Group I

ABSTRACT The bacterial candidate phylum Termite Group I (TG-1) presently consists mostly of “Endomicrobia,” which are endosymbionts of flagellate protists occurring exclusively in the hindguts of termites and wood-feeding cockroaches. Here, we show that public databases contain many, mostly undocumented 16S rRNA gene sequences from other habitats that are affiliated with the TG-1 phylum but are only distantly related to “Endomicrobia.” Phylogenetic analysis of the expanded data set revealed several diverse and deeply branching lineages comprising clones from many different habitats. In addition, we designed specific primers to explore the diversity and environmental distribution of bacteria in the TG-1 phylum.

Overestimation of Streptococcus mutans prevalence by nested PCR detection of the 16S rRNA gene

2006 ◽  
Vol 55 (1) ◽  
pp. 109-113 ◽  
Author(s):  
Ali Al-Ahmad ◽  
Thorsten Mathias Auschill ◽  
Gabriele Braun ◽  
Elmar Hellwig ◽  
Nicole Birgit Arweiler
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Streptococcus Mutans ◽  
Nested Pcr ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Direct Pcr ◽  
Specific Primers ◽  
The 16S Rrna Gene

This study was carried out in order to compare two PCR-based methods in the detection of Streptococcus mutans. The first PCR method was based on primers for the 16S rRNA gene and the second method was based on specific primers that targeted the glucosyltransferase gene (gtfB). Each PCR was performed with eight different streptococci from the viridans group, five other streptococci and 17 different non-streptococcal bacterial strains. Direct use of the S. mutans 16S rRNA gene-specific primers revealed that Streptococcus gordonii and Streptococcus infantis were also detected. After amplifying the 16S rRNA gene with universal primers and subsequently performing nested PCR, the S. mutans-specific nested primers based on the 16S rRNA gene detected all tested streptococci. There was no cross-reaction of the gtfB primers after direct PCR. Our results indicate that direct PCR and nested PCR based on 16S rRNA genes can reveal false-positive results for oral streptococci and lead to an overestimation of the prevalence of S. mutans with regards to its role as the most prevalent causative agent of dental caries.

Characterization of fecal microbiota in cats using universal 16S rRNA gene and group-specific primers for Lactobacillus and Bifidobacterium spp.

2010 ◽  
Vol 144 (1-2) ◽  
pp. 140-146 ◽  
Author(s):  
Lauren E. Ritchie ◽  
Kathrin F. Burke ◽  
Jose F. Garcia-Mazcorro ◽  
Jörg M. Steiner ◽  
Jan S. Suchodolski
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Specific Primers

Improved group-specific primers based on the full SILVA 16S rRNA gene reference database

2014 ◽  
Vol 16 (8) ◽  
pp. 2389-2407 ◽  
Author(s):  
Stefan Pfeiffer ◽  
Milica Pastar ◽  
Birgit Mitter ◽  
Kathrin Lippert ◽  
Evelyn Hackl ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Reference Database ◽  
Rrna Gene ◽  
Specific Primers

Denaturing Gradient Gel Electrophoresis Detects Bacterial and Cyaonbacterial Diversities in Biological Soil Crusts in a Semiarid Desert, China

2013 ◽  
Vol 726-731 ◽  
pp. 3680-3684
Author(s):  
Ying Zhang ◽  
Cheng You Cao ◽  
Peng Zhang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gel Electrophoresis ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Biological Soil Crusts ◽  
Rrna Gene ◽  
Sandy Land ◽  
Specific Primers ◽  
Soil Crusts ◽  
Gradient Gel Electrophoresis

The purpose of this study is to assess the application of denaturing gradient gel electrophoresis (DGGE) for analyzing the bacterial and cyanobacterial diversities of biological soil crusts (BSCs) in sandy land. Soil microbial DNA was extracted from BSCs under different plantations in Horqin Sandy Land of Northeast China. 16S rRNA gene fragments from bacteria and cyanobacteria were amplified by universal bacterial and cyanobacteria-specific primers. Fourteen and six prominent bands were detected in the bacterial and cyanobacterial DGGE profiles, respectively. These bands were excised, cloned and sequenced. Phylogenetic analysis classified the bacterial sequences into the following main groups:Escherichia,Bacillus,Paenibacillus,Shigella, andPseudomonas. The cyanobacterial sequences were classified asMicrocoleus,LeptolyngbyaandHaslea. Our study suggests that DGGE is a useful technique for detecting dominant species compositions of bacterial and cyanobacterial communities in biological soil crusts, and specific primers are recommended for PCR of 16S rRNA gene fragments.

scholarly journals Use of 16S rRNA Gene-Targeted Group-Specific Primers for Real-Time PCR Analysis of Predominant Bacteria in Mouse Feces

2015 ◽  
Vol 81 (19) ◽  
pp. 6749-6756 ◽  
Author(s):  
Yun-Wen Yang ◽  
Mang-Kun Chen ◽  
Bing-Ya Yang ◽  
Xian-Jie Huang ◽  
Xue-Rui Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Real Time ◽  
Real Time Pcr ◽  
Bacterial Species ◽  
Chronic Inflammatory Bowel Disease ◽  
Trinitrobenzene Sulfonic Acid ◽  
Rrna Gene ◽  
Specific Primers ◽  
Content Type

ABSTRACTMouse models are widely used for studying gastrointestinal (GI) tract-related diseases. It is necessary and important to develop a new set of primers to monitor the mouse gut microbiota. In this study, 16S rRNA gene-targeted group-specific primers forFirmicutes,Actinobacteria,Bacteroidetes,Deferribacteres, “CandidatusSaccharibacteria,”Verrucomicrobia,Tenericutes, andProteobacteriawere designed and validated for quantification of the predominant bacterial species in mouse feces by real-time PCR. After confirmation of their accuracy and specificity by high-throughput sequencing technologies, these primers were applied to quantify the changes in the fecal samples from a trinitrobenzene sulfonic acid-induced colitis mouse model. Our results showed that this approach efficiently predicted the occurrence of colitis, such as spontaneous chronic inflammatory bowel disease in transgenic mice. The set of primers developed in this study provides a simple and affordable method to monitor changes in the intestinal microbiota at the phylum level.

scholarly journals Distribution of Bifidobacterial Species in Human Intestinal Microflora Examined with 16S rRNA-Gene-Targeted Species-Specific Primers

1999 ◽  
Vol 65 (10) ◽  
pp. 4506-4512 ◽  
Author(s):  
Takahiro Matsuki ◽  
Koichi Watanabe ◽  
Ryuichiro Tanaka ◽  
Masafumi Fukuda ◽  
Hiroshi Oyaizu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Intestinal Tract ◽  
Bifidobacterium Longum ◽  
Rrna Gene ◽  
Human Feces ◽  
Specific Primers ◽  
Specific Pcr ◽  
Species Specific ◽  
Human Intestinal Tract

ABSTRACT In order to clarify the distribution of bifidobacterial species in the human intestinal tract, a 16S rRNA-gene-targeted species-specific PCR technique was developed and used with DNAs extracted from fecal samples obtained from 48 healthy adults and 27 breast-fed infants. To cover all of the bifidobacterial species that have been isolated from and identified in the human intestinal tract, species-specific primers for Bifidobacterium longum, B. infantis,B. dentium, and B. gallicum were developed and used with primers for B. adolescentis, B. angulatum, B. bifidum, B. breve, and the B. catenulatum group (B. catenulatum andB. pseudocatenulatum) that were developed in a previous study (T. Matsuki, K. Watanabe, R. Tanaka, and H. Oyaizu, FEMS Microbiol. Lett. 167:113–121, 1998). The specificity of the nine primers was confirmed by PCR, and the species-specific PCR method was found to be a useful means for identifying Bifidobacteriumstrains isolated from human feces. The results of an examination of bifidobacterial species distribution showed that the B. catenulatum group was the most commonly found taxon (detected in 44 of 48 samples [92%]), followed by B. longum andB. adolescentis, in the adult intestinal bifidobacterial flora and that B. breve, B. infantis, andB. longum were frequently found in the intestinal tracts of infants. The present study demonstrated that qualitative detection of the bifidobacterial species present in human feces can be accomplished rapidly and accurately.

scholarly journals Selection of specific primers based on 16s rRNA gene for Bacillus cereus bacteria

2018 ◽  
pp. 196-201
Author(s):  
N.A. Feoktistova ◽  
◽  
D.A. Vasiliev ◽  
A.V. Mastilenko ◽  
◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacillus Cereus ◽  
Rrna Gene ◽  
Specific Primers ◽  
Selection Of

scholarly journals Development of 16S rRNA-Gene-Targeted Group-Specific Primers for the Detection and Identification of Predominant Bacteria in Human Feces

2002 ◽  
Vol 68 (11) ◽  
pp. 5445-5451 ◽  
Author(s):  
Takahiro Matsuki ◽  
Koichi Watanabe ◽  
Junji Fujimoto ◽  
Yukiko Miyamoto ◽  
Toshihiko Takada ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Intestinal Microflora ◽  
Quantitative Detection ◽  
Rrna Gene ◽  
Human Feces ◽  
Specific Primers ◽  
Specific Pcr ◽  
Detection And Identification ◽  
Bacterial Groups

ABSTRACT For the detection and identification of predominant bacteria in human feces, 16S rRNA-gene-targeted group-specific primers for the Bacteroides fragilis group, Bifidobacterium, the Clostridium coccoides group, and Prevotella were designed and evaluated. The specificity of these primers was confirmed by using DNA extracted from 90 species that are commonly found in the human intestinal microflora. The group-specific primers were then used for identification of 300 isolates from feces of six healthy volunteers. The isolates were clearly identified as 117 isolates of the B. fragilis group, 22 isolates of Bifidobacterium, 65 isolates of the C. coccoides group, and 17 isolates of Prevotella, indicating that 74% of the isolates were identified with the four pairs of primers. The remaining 79 isolates were identified by 16S ribosomal DNA sequence analysis and consisted of 40 isolates of Collinsella, 24 isolates of the Clostridium leptum subgroup, and 15 isolates of disparate clusters. In addition, qualitative detection of these bacterial groups was accomplished without cultivation by using DNA extracted from the fecal samples. The goal for this specific PCR technique is to develop a procedure for quantitative detection of these bacterial groups, and a real-time quantitative PCR for detection of Bifidobacterium is now being investigated (T. Requena, J. Burton, T. Matsuki, K. Munro, M. A. Simon, R. Tanaka, K. Watanabe, and G. W. Tannock, Appl. Environ. Microbiol. 68:2420-2427, 2002). Therefore, the approaches used to detect and identify predominant bacteria with the group-specific primers described here should contribute to future studies of the composition and dynamics of the intestinal microflora.

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